Army Chaplain Scott Squires has been to battles all over the world -- but he never imagined he'd be fighting his biggest one right here at home. For Squires, who's spent 25 years serving his country, no one was more surprised than he was that the same military who hired him for his faith is now punishing him for exercising it. Turns out, some Obama-era habits are hard to break.

Like a lot of chaplains, Scott watched the military change under the last administration. He saw morale tank. He heard the unbelievable stories of airmen, sailors, and Marines who were targeted for their faith. And until Wes Modder nearly lost his job, he might have thought military chaplains were safe. Squires found out this year how wrong he was. The administration may have changed, but the intolerant attitudes of some have not.

When he was transferred to Fort Bragg last year, Squires picked up where he'd left off at other bases with the Army's Strong Bonds program. For years, he'd been speaking at the event, trying to help soldiers develop healthier relationships in a stressful military life that's led to some of the highest divorce rates in the country. When a lesbian couple wanted to join the marriage retreat, Scott realized he couldn't, in good conscience, participate. So, he did what Army regulations demanded: he found another chaplain to oversee it.

Now, even though he followed Army policy, he could lose his job! To this couple, Scott's actions weren't an accommodation, they were "discrimination." An official military investigation was launched -- and Squires, despite his chaplain status, is being recommended for discipline! "The Army E.O. policy states that no service will be denied to any member of the Armed Service, regardless of race, color, national origin, gender, religious affiliation, or sexual orientation," the report reads. "CH Squires should be reprimanded for his failure to include (name deleted) in the initial Strong Bonds Retreat."

Asked how he was taking the news, Squires said he was "shocked." After all, his attorneys at First Liberty point out, he was following the Army's own policy! He couldn't lead the session, so he found someone who could. If anything, this should be a lesson in the art of compromise. His solution accomplished the perfect balance of accommodating his faith and serving these women. Even so, he points out, "...[T]he investigator concluded that I should be reprimanded for doing something I'm required to do under Army regulations and my endorser's rules. I hope the Army sees that I was simply following Army regulations and the tenets of my church."

Remember when the Pentagon said religious liberty wouldn't be a casualty of open homosexuality in the military? So do we. Unfortunately, it's just another broken promise of the same-sex marriage movement. Now, because of the culture of hostility created in the military under Obama, the Army refuses to accept a compromise that should have satisfied everyone. But, as we should all know by now, the Left isn't interested in coexistence. Instead, it wants to punish a father of three, who served multiple tours in Afghanistan, Africa, and the Middle East.

And of course, there's the other piece of this, which is Chaplain Squires's sponsoring organization: the Southern Baptist Convention. As Fox News's Todd Starnes explains, the SBC's North American Mission Board (NAMB) doesn't support same-sex marriage -- and its 2013 memo reiterated as much. "NAMB endorsed chaplains will not conduct or attend a wedding ceremony for any same sex couple, bless such a union or perform counseling in support of such a union, assist or support paid contractors or volunteers leading same-sex relational events, nor offer any kind of relationship training or retreat, on or off a military installation, that would give the appearance of accepting the homosexual lifestyle or sexual wrongdoing." He's not only bound by his own conviction -- but the conviction of his military sponsors. And yet, this investigator thinks Chaplain Squires should be punished just for explaining his beliefs to the offended soldier!

Mike Berry, Squires's attorney at First Liberty, can't believe the terrible precedent this would set. "That would mean a chaplain can't even talk about their religious beliefs without being accused of discrimination. That would strip thousands of chaplains across our military of their most basic freedoms under the First Amendment." Something this president, who's fought to restore religious liberty, would never stand for.

As FRC's own Lt. General Jerry Boykin has said, "If the military wants a chaplain corps, then they have to be prepared for chaplains to be chaplains. A chaplain isn't worth anything if he isn't allowed to minister and counsel according to his faith. If the Army won't allow him to be a chaplain, then he becomes nothing more than a social worker."

If anyone should be free to exercise their faith, shouldn't it be chaplains? It's time for the Army to refresh its memory on a little thing called the First Amendment and reread the president's executive order on religious liberty. Both documents ought to be all the proof they need that Chaplain Squires is guilty of nothing but doing his job. And, by all accounts, doing it well.

Tony Perkins' Washington Update is written with the aid of FRC senior writers.